Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 24
Found at i:2924100 original size:18 final size:18
Alignment explanation
Indices: 2924062--2924107 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
2924052 CAAGCTGTCA
*
2924062 ATGAAGATGAAGCTGACG
1 ATGAAGATGAAGATGACG
* *
2924080 ATGAAGATGACGATGATG
1 ATGAAGATGAAGATGACG
*
2924098 ATGATGATGA
1 ATGAAGATGA
2924108 TGATCCAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.22
Consensus pattern (18 bp):
ATGAAGATGAAGATGACG
Found at i:2925949 original size:183 final size:185
Alignment explanation
Indices: 2925491--2926023 Score: 932
Period size: 185 Copynumber: 2.9 Consensus size: 185
2925481 ATATCAGCAT
*
2925491 AAAA-TGTCGATACCTTTTCAAAACGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGT
1 AAAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGT
* *
2925555 AATAGGTAATTTTGTAATATAACCGATATAGATATACCGGTTTTATGAGAGAATAGGTCTACAAC
66 AATAGGTAATTTTGTAATATAACCGGTATAGATATACTGGTTTTATGAGAGAATAGGTCTACAAC
2925620 CTATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
131 CTATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
**
2925675 AAAAGTGTATATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGT
1 AAAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGT
*
2925740 AATAGGTAATTTTGTAATATAACCGGTATAGATATACTGGTTTTATGAGAGAATAGGTATACAAC
66 AATAGGTAATTTTGTAATATAACCGGTATAGATATACTGGTTTTATGAGAGAATAGGTCTACAAC
2925805 CTATATCGACACTTTTTAATATTGTGTCGCTACTTTATGT-CAGAATGGATG-AA
131 CTATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
*
2925858 AAAAGTGTCGATACATTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGT
1 AAAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGT
* *
2925923 AATATGTAATTTTGTAATATAACCGGTATAAATATACCT-GTTTTATGAGAGAATAGGTCTACAA
66 AATAGGTAATTTTGTAATATAACCGGTATAGATATA-CTGGTTTTATGAGAGAATAGGTCTACAA
2925987 CCTATATCGACACTTTTTAATATTGTGTC-CATACTTT
130 CCTATATCGACACTTTTTAATATTGTGTCGC-TACTTT
2926024 TAAGTAACGC
Statistics
Matches: 334, Mismatches: 12, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
182 1 0.00
183 157 0.47
184 17 0.05
185 159 0.48
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.34
Consensus pattern (185 bp):
AAAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGT
AATAGGTAATTTTGTAATATAACCGGTATAGATATACTGGTTTTATGAGAGAATAGGTCTACAAC
CTATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
Found at i:2928914 original size:22 final size:22
Alignment explanation
Indices: 2928870--2928914 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2928860 ATTACATAAC
*
2928870 TTTAAAAAAAGTATAGATCCTT
1 TTTAAAAAAAGTATAGAACCTT
*
2928892 TTTATAAAAAGTAT-GAACACTT
1 TTTAAAAAAAGTATAGAAC-CTT
2928914 T
1 T
2928915 CAACATATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTAAAAAAAGTATAGAACCTT
Found at i:2929055 original size:23 final size:23
Alignment explanation
Indices: 2929024--2929073 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
2929014 ATAGATAAAA
*
2929024 ATATGATGTAATAGGTAACGCTT
1 ATATAATGTAATAGGTAACGCTT
*
2929047 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAACGCTT
2929070 ATAT
1 ATAT
2929074 TGTAAAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (23 bp):
ATATAATGTAATAGGTAACGCTT
Found at i:2929834 original size:12 final size:12
Alignment explanation
Indices: 2929812--2929857 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
2929802 CAAGTTGTCA
*
2929812 ATGAAGATGAAG
1 ATGACGATGAAG
*
2929824 CTGACGATGAAG
1 ATGACGATGAAG
*
2929836 ATGACGATGATG
1 ATGACGATGAAG
*
2929848 ATGATGATGA
1 ATGACGATGA
2929858 TGATCCAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.22
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:2929850 original size:18 final size:18
Alignment explanation
Indices: 2929812--2929857 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
2929802 CAAGTTGTCA
*
2929812 ATGAAGATGAAGCTGACG
1 ATGAAGATGAAGATGACG
* *
2929830 ATGAAGATGACGATGATG
1 ATGAAGATGAAGATGACG
*
2929848 ATGATGATGA
1 ATGAAGATGA
2929858 TGATCCAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.22
Consensus pattern (18 bp):
ATGAAGATGAAGATGACG
Found at i:2931562 original size:185 final size:183
Alignment explanation
Indices: 2931250--2931615 Score: 669
Period size: 185 Copynumber: 2.0 Consensus size: 183
2931240 TAAAATGTCG
*
2931250 ATACCTTTTCAAAACGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGGTAAT
1 ATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGGTAAT
*
2931315 TTTGTAATATAACCGATATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGAC
66 TTTGTAATATAACCGATATAGATATACCGGTTTTATGAGAGAATAGGTATACAACCTATATCGAC
2931380 ACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAAAAAAGTGTAT
131 ACTTTTTAATATTGTGTCGCTACTTTATGT-CAGAATGGATG-AAAAAAGTGTAT
2931435 ATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGGTAAT
1 ATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGGTAAT
* * *
2931500 TTTGTAATATAACCGGTATATATATACTGGTTTTATGAGAGAATAGGTATACAACCTATATCGAC
66 TTTGTAATATAACCGATATAGATATACCGGTTTTATGAGAGAATAGGTATACAACCTATATCGAC
2931565 ACTTTTTAATATTGTGTCGCTACTTTATGTCAGAATGGATGAAAAAAGTGT
131 ACTTTTTAATATTGTGTCGCTACTTTATGTCAGAATGGATGAAAAAAGTGT
2931616 CGATTGAAAA
Statistics
Matches: 176, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
183 10 0.06
184 11 0.06
185 155 0.88
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (183 bp):
ATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGGTAAT
TTTGTAATATAACCGATATAGATATACCGGTTTTATGAGAGAATAGGTATACAACCTATATCGAC
ACTTTTTAATATTGTGTCGCTACTTTATGTCAGAATGGATGAAAAAAGTGTAT
Found at i:2931717 original size:162 final size:162
Alignment explanation
Indices: 2931445--2931752 Score: 548
Period size: 162 Copynumber: 1.9 Consensus size: 162
2931435 ATACCTTTTC
2931445 AAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGGTAATTTTGTAATAT
1 AAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGGTAATTTTGTAATAT
* * *
2931510 AACCGGTATATATATACTGGTTTTATGAGAGAATAGGTATACAACCTATATCGACACTTTTTAAT
66 AACCGGTATAAATATACTGGTTTTATGAGAGAATAGGTATACAACCTATATCGACACATTTTAAC
2931575 ATTGTGTCGC-TACTTTATGTCAGAATGGATGA
131 ATTGTGTC-CATACTTTATGTCAGAATGGATGA
2931607 AAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGGTAATTTTGTAATAT
1 AAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGGTAATTTTGTAATAT
*
2931672 AACCGGTATAAATATACCT-GTTTTATGAGAGAATAGGTCTACAACCTATATCGACACATTTTAA
66 AACCGGTATAAATATA-CTGGTTTTATGAGAGAATAGGTATACAACCTATATCGACACATTTTAA
2931736 CATTGTGTCCATACTTT
130 CATTGTGTCCATACTTT
2931753 TAAGTAACGC
Statistics
Matches: 140, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
161 1 0.01
162 137 0.98
163 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (162 bp):
AAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGGTAATTTTGTAATAT
AACCGGTATAAATATACTGGTTTTATGAGAGAATAGGTATACAACCTATATCGACACATTTTAAC
ATTGTGTCCATACTTTATGTCAGAATGGATGA
Found at i:2934601 original size:22 final size:22
Alignment explanation
Indices: 2934557--2934601 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2934547 ATTACATAAC
*
2934557 TTTAAAAAAAGTATAGATCCTT
1 TTTAAAAAAAGTATAGAACCTT
*
2934579 TTTATAAAAAGTAT-GAACACTT
1 TTTAAAAAAAGTATAGAAC-CTT
2934601 T
1 T
2934602 CAACATATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTAAAAAAAGTATAGAACCTT
Found at i:2934742 original size:23 final size:23
Alignment explanation
Indices: 2934711--2934760 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
2934701 ATAGATAAAA
*
2934711 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
2934734 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
2934757 ATAT
1 ATAT
2934761 TGTAAAGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:2935648 original size:23 final size:23
Alignment explanation
Indices: 2935619--2935666 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
2935609 AAATAGGTCA
*
2935619 ATATAAGCGCTACCTATTATATT
1 ATATAAGCGCTACCTAATATATT
*
2935642 ATATAAGCGCTACCTAATATGTT
1 ATATAAGCGCTACCTAATATATT
2935665 AT
1 AT
2935667 TGTATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATATATT
Found at i:2935717 original size:87 final size:87
Alignment explanation
Indices: 2935619--2935781 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
2935609 AAATAGGTCA
* *
2935619 ATATAAGCGCTACCTATTATATTATATAAGCGCTACCTAATATGTTATTGTATTTAATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
2935684 CCGGTTAAATACCTATTTTATT
66 CCGGTTAAATACCTATTTTATT
* *
2935706 ATATAAGCGCTATCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
*
2935771 CTGGTTAAATA
66 CCGGTTAAATA
2935782 ATATAACATA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
CCGGTTAAATACCTATTTTATT
Found at i:2935753 original size:23 final size:23
Alignment explanation
Indices: 2935703--2935747 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2935693 TACCTATTTT
* *
2935703 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
2935726 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
2935748 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:2937249 original size:23 final size:24
Alignment explanation
Indices: 2937204--2937250 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2937194 TTTATATTTA
*
2937204 ATTTTTATTTATAATTTTCAAATT
1 ATTTTAATTTATAATTTTCAAATT
2937228 ATTTTAATTTA-ATATTTT-AAATT
1 ATTTTAATTTATA-ATTTTCAAATT
2937251 CTTAATTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTAATTTATAATTTTCAAATT
Found at i:2937263 original size:16 final size:16
Alignment explanation
Indices: 2937244--2937302 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 16
2937234 ATTTAATATT
2937244 TTAAATTCTTAATTTC
1 TTAAATTCTTAATTTC
* *
2937260 TTAAATT-TTACTTCC
1 TTAAATTCTTAATTTC
* *
2937275 ATAACATTCTAAATTT-
1 TTAA-ATTCTTAATTTC
*
2937291 TTAATTTCTTAA
1 TTAAATTCTTAA
2937303 ATTATTTCAC
Statistics
Matches: 32, Mismatches: 9, Indels: 5
0.70 0.20 0.11
Matches are distributed among these distances:
15 15 0.47
16 13 0.41
17 4 0.12
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATTCTTAATTTC
Found at i:2937323 original size:39 final size:39
Alignment explanation
Indices: 2937210--2937328 Score: 120
Period size: 39 Copynumber: 3.1 Consensus size: 39
2937200 TTTAATTTTT
* * * *
2937210 ATTTATAATTT-TCAAATTATTTTA-ATTTAATATTTTAA
1 ATTTTTAATTTCTTAAATTATTTCACA-TTAATATTCTAA
* * *
2937248 ATTCTTAATTTCTTAAATTTTACTTC-CA-TAACATTCTAA
1 ATTTTTAATTTCTTAAA--TTATTTCACATTAATATTCTAA
2937287 ATTTTTAATTTCTTAAATTATTTCACATTAATATTCTAA
1 ATTTTTAATTTCTTAAATTATTTCACATTAATATTCTAA
2937326 ATT
1 ATT
2937329 ATTATTTAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 11
0.76 0.12 0.13
Matches are distributed among these distances:
37 6 0.09
38 11 0.17
39 42 0.65
41 6 0.09
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (39 bp):
ATTTTTAATTTCTTAAATTATTTCACATTAATATTCTAA
Found at i:2937389 original size:25 final size:24
Alignment explanation
Indices: 2937360--2937406 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
2937350 AACTTCCAAA
2937360 TACTTGAA-ATTTAATTATATTTTTT
1 TACTT-AATATTTAA-TATATTTTTT
2937385 TACTTAATATTTAATATATTTT
1 TACTTAATATTTAATATATTTT
2937407 CTTTCAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (24 bp):
TACTTAATATTTAATATATTTTTT
Found at i:2937491 original size:2 final size:2
Alignment explanation
Indices: 2937484--2937516 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2937474 TAGAATTTTC
2937484 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2937517 ATTTAAAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2938086 original size:60 final size:60
Alignment explanation
Indices: 2938015--2938130 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 60
2938005 AGATACCTAT
* ** *
2938015 TTTTTATG-AAAATTCTTTAGGCACCAAAAGTCAATTTGAGATATAAATTTAGGCACTTAC
1 TTTTTACGAAAAATTCTTTAAACACCAAAAATCAATTTGAGATAT-AATTTAGGCACTTAC
*
2938075 TTTTTACGAAAAATTCTTTAAACACCAAAAATCAATTTGAGGTATAATTTAGGCAC
1 TTTTTACGAAAAATTCTTTAAACACCAAAAATCAATTTGAGATATAATTTAGGCAC
2938131 CTAAAGGTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
60 18 0.36
61 32 0.64
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (60 bp):
TTTTTACGAAAAATTCTTTAAACACCAAAAATCAATTTGAGATATAATTTAGGCACTTAC
Found at i:2945942 original size:138 final size:137
Alignment explanation
Indices: 2945655--2946591 Score: 1325
Period size: 138 Copynumber: 6.8 Consensus size: 137
2945645 GGTGATGTTC
* * * *
2945655 CAACTCCGTATGCGATGGAAACAAGTTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
1 CAACTCCATATGCGAT-GAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-
** * * *
2945720 CCTCATT-GGATGAGTTTTTCTCATTATGAACT-TTCCACTGAAAATGTTGATTCCTCGAGTGAG
64 CCTTTTTCGGATGAGTTCTTCTCATTATGAACTCTT---CTGGAAATGTTGATCCCTCGAGTGAG
*
2945783 GTGTTGCTGATT
126 GCGTTGCTGATT
2945795 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
1 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-C
* * *
2945860 CTTTTTCGGATGAGTTATTCTCATTATGAACTCTTATGGAAATGTTGATCCCTCGAGTGAGGTGT
65 CTTTTTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCCTCGAGTGAGGCGT
*
2945925 TGTTGATT
130 TGCTGATT
*
2945933 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTTC
1 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TC
*
2945998 TTTTTTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCCTCGAGTGAGGCGT
65 CTTTTTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCCTCGAGTGAGGCGT
*
2946063 TGCTGATG
130 TGCTGATT
* * * *
2946071 CAACTCCATATGTGATGAATCAAGTTAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCC
1 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* *
2946136 TTTAGTCGGATGAGTTCTTCTCATTATGAAATCTTCTGGAAATGTTGATCCCT----TGAGGCGT
66 TTT-TTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCCTCGAGTGAGGCGT
*
2946197 TGTTGATT
130 TGCTGATT
* * * * *
2946205 CAACTCCATATGCGATGAATCGATCTAAGTTTGAATAAGGTCTTCTCATTATGAACTTATTCTCC
1 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* *
2946270 TTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAAAGTTGATTCCTCGAGTGAGGCGT
66 TTTT-TCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCCTCGAGTGAGGCGT
*
2946335 TGTTGATT
130 TGCTGATT
* * *
2946343 AAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGCATTTCTTCTCC
1 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * * *
2946408 TTTTGTTGGATGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTTGATCCCTCGAGTGAAGTGT
66 TTTT-TCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCCTCGAGTGAGGCGT
*
2946473 TGCTCATT
130 TGCTGATT
* *
2946481 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCAGTATGAA---CTTCTCC
1 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
*
2946543 TTTTGTCGGATGAGTTCTTCTCATTTTGAACTCTTCTGGAAATGTTGAT
66 TTTT-TCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGAT
2946592 TCACCTCCTT
Statistics
Matches: 725, Mismatches: 63, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
134 119 0.16
135 53 0.07
137 5 0.01
138 456 0.63
139 51 0.07
140 39 0.05
141 2 0.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (137 bp):
CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
TTTTTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCCTCGAGTGAGGCGTT
GCTGATT
Found at i:2946336 original size:272 final size:271
Alignment explanation
Indices: 2945655--2946593 Score: 1293
Period size: 272 Copynumber: 3.4 Consensus size: 271
2945645 GGTGATGTTC
* * * *
2945655 CAACTCCGTATGCGATGGAAACAAGTTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
1 CAACTCCATATGCGAT-GAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-
** *
2945720 CCTCAT-T-GGATGAGTTTTTCTCATTATGAACT-TTCCACT-GAAAATGTTGATTCCTCGAGTG
64 CCTTTTGTCGGATGAGTTCTTCTCATTATGAACTCTT---CTGGAAAA-GTTGATTCCTCGAGTG
*
2945781 AGGTGTTGCTGATTCAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTA
125 AGGCGTTGCTGATTCAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTA
* * * *
2945846 TGAACTTCTTCTCCCTTTTTCGGATGAGTTATTCTCATTATGAACTCTTATGGAAATGTTGATCC
190 TGAACTTTTTCT-CCTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCC
*
2945911 CTCGAGTGAGGTGTTGTTGATT
254 CT----TGAGGAGTTGTTGATT
* *
2945933 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTTC
1 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * *
2945998 TTTTTTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCCTCGAGTGAGGCGT
66 TTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAAAGTTGATTCCTCGAGTGAGGCGT
* * * *
2946063 TGCTGATGCAACTCCATATGTGATGAATCAAGTTAAGGTTGAACAAGTTCTTCTCATTATGAACT
131 TGCTGATTCAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACT
*
2946128 TTTTCTCCTTTAGTCGGATGAGTTCTTCTCATTATGAAATCTTCTGGAAATGTTGATCCCTTGAG
196 TTTTCTCCTTT-GTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCCTTGAG
*
2946193 GCGTTGTTGATT
260 GAGTTGTTGATT
* * * * *
2946205 CAACTCCATATGCGATGAATCGATCTAAGTTTGAATAAGGTCTTCTCATTATGAACTTATTCTCC
1 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
2946270 TTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAAAGTTGATTCCTCGAGTGAGGCGT
66 TTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAAAGTTGATTCCTCGAGTGAGGCGT
* * *
2946335 TGTTGATTAAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGCA-T
131 TGCTGATTCAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACT
* * *
2946399 TTCTTCTCCTTTTGTTGGATGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTTGATCCCTCGA
196 TT-TTCTCC-TTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCCTTGA
2946464 GTGAAG-TGTTGCTCATT
259 G-G-AGTTGTTG---ATT
* *
2946481 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCAGTATGAA---CTTCTCC
1 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* *
2946543 TTTTGTCGGATGAGTTCTTCTCATTTTGAACTCTTCTGGAAATGTTGATTC
66 TTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAAAGTTGATTC
2946594 ACCTCCTTCT
Statistics
Matches: 596, Mismatches: 53, Indels: 29
0.88 0.08 0.04
Matches are distributed among these distances:
271 3 0.01
272 246 0.41
273 64 0.11
274 1 0.00
275 5 0.01
276 188 0.32
277 48 0.08
278 39 0.07
279 2 0.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (271 bp):
CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
TTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAAAGTTGATTCCTCGAGTGAGGCGT
TGCTGATTCAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACT
TTTTCTCCTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCCTTGAGG
AGTTGTTGATT
Found at i:2947559 original size:16 final size:16
Alignment explanation
Indices: 2947534--2947582 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
2947524 CGAACCCTCA
2947534 TTTTTC-TTTTCATTT
1 TTTTTCTTTTTCATTT
2947549 TTTTTCTTTTTTC-TTT
1 TTTTTC-TTTTTCATTT
2947565 TTTTCTCTTTTTCATTT
1 TTTT-TCTTTTTCATTT
2947582 T
1 T
2947583 CATTTTGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.20
16 13 0.43
17 11 0.37
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTCTTTTTCATTT
Found at i:2947566 original size:17 final size:17
Alignment explanation
Indices: 2947540--2947582 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
2947530 CTCATTTTTC
*
2947540 TTTTCATTTTTTTTCTT
1 TTTTCATTTTTTCTCTT
*
2947557 TTTTCTTTTTTTCTC-T
1 TTTTCATTTTTTCTCTT
2947573 TTTTCATTTT
1 TTTTCATTTT
2947583 CATTTTGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTCATTTTTTCTCTT
Found at i:2947609 original size:21 final size:20
Alignment explanation
Indices: 2947559--2947610 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
2947549 TTTTTCTTTT
2947559 TTCTTTTTTTCTCTTTTTCA
1 TTCTTTTTTTCTCTTTTTCA
*
2947579 TT-TTCATTTTGCAT-TTTTTCA
1 TTCTT--TTTTTC-TCTTTTTCA
2947600 TTCTTTTTTTC
1 TTCTTTTTTTC
2947611 AAGCATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
19 2 0.08
20 7 0.27
21 14 0.54
22 3 0.12
ACGTcount: A:0.08, C:0.17, G:0.02, T:0.73
Consensus pattern (20 bp):
TTCTTTTTTTCTCTTTTTCA
Found at i:2954205 original size:32 final size:31
Alignment explanation
Indices: 2954128--2954276 Score: 133
Period size: 32 Copynumber: 4.8 Consensus size: 31
2954118 GGACCTATCT
* * * *
2954128 ATATATTCCGAAGAACTTAGGTAA-CTGTCC
1 ATATGTTCCAAAGAACATAGGTAATCTGACC
*** *
2954158 ATATGTTCTGGAGAACATAGGTAATCCTGACG
1 ATATGTTCCAAAGAACATAGGTAAT-CTGACC
* *
2954190 ATATGTTCCAAAGAACATAGGTAATTTTGTCC
1 ATATGTTCCAAAGAACATAGGTAA-TCTGACC
*
2954222 ATATGTTCCGAAGAACATAGGTAATCT-ATCC
1 ATATGTTCCAAAGAACATAGGTAATCTGA-CC
*
2954253 ATATGTCTCGAAAG-ACATAGGTAA
1 ATATGT-TCCAAAGAACATAGGTAA
2954277 CCATCGACTC
Statistics
Matches: 97, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
30 20 0.21
31 20 0.21
32 56 0.58
33 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (31 bp):
ATATGTTCCAAAGAACATAGGTAATCTGACC
Found at i:2954237 original size:64 final size:61
Alignment explanation
Indices: 2954122--2954277 Score: 172
Period size: 64 Copynumber: 2.5 Consensus size: 61
2954112 CCCGAAGGAC
* * * * * *
2954122 CTATCTATATATTCCGAAGAACTTAGGTAACTGTCCATATGTTCTGGAGAACATAGGTAAT
1 CTATCCATATGTTCCAAAGAACATAGGTAACTGTCCATATGTTCCGAAGAACATAGGTAAT
* *
2954183 CCTGA-CGATATGTTCCAAAGAACATAGGTAATTTTGTCCATATGTTCCGAAGAACATAGGTAAT
1 -CT-ATCCATATGTTCCAAAGAACATAGGTAA--CTGTCCATATGTTCCGAAGAACATAGGTAAT
*
2954247 CTATCCATATGTCTCGAAAG-ACATAGGTAAC
1 CTATCCATATGT-TCCAAAGAACATAGGTAAC
2954278 CATCGACTCT
Statistics
Matches: 79, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
62 25 0.32
63 20 0.25
64 34 0.43
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (61 bp):
CTATCCATATGTTCCAAAGAACATAGGTAACTGTCCATATGTTCCGAAGAACATAGGTAAT
Found at i:2954856 original size:2 final size:2
Alignment explanation
Indices: 2954788--2954837 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2954778 TTATCACATT
2954788 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2954830 TA TA TA TA
1 TA TA TA TA
2954838 CACAACTCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2955413 original size:20 final size:20
Alignment explanation
Indices: 2955388--2955439 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
2955378 AATGAAGGTA
2955388 TGTATCGATGCACCCTACAG
1 TGTATCGATGCACCCTACAG
2955408 TGTATCGATGCACCCTACAG
1 TGTATCGATGCACCCTACAG
2955428 TGTATCGATGCA
1 TGTATCGATGCA
2955440 TTCCTTAACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (20 bp):
TGTATCGATGCACCCTACAG
Found at i:2972163 original size:24 final size:24
Alignment explanation
Indices: 2972133--2972188 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
2972123 TAGAAGTTCG
2972133 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
2972157 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
2972181 ATTGAAGC
1 ATTGAAGC
2972189 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:2973002 original size:20 final size:19
Alignment explanation
Indices: 2972933--2973007 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 19
2972923 AATGTAATTT
2972933 GTGTACCGATACA-TAGGCA
1 GTGTACCGATACACTAGG-A
2972952 GTGTACCGATACACCAGTTAAGGA
1 GTGTACCGATACA-C---T-AGGA
*
2972976 ATGTACCGATACACTATGGA
1 GTGTACCGATACACTA-GGA
2972996 GTGTACCGATAC
1 GTGTACCGATAC
2973008 CTACCTTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
19 14 0.30
20 15 0.32
23 1 0.02
24 14 0.30
25 3 0.06
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (19 bp):
GTGTACCGATACACTAGGA
Found at i:2974554 original size:23 final size:23
Alignment explanation
Indices: 2974528--2974580 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
2974518 TATGGCACAA
2974528 CGGTGCAACTCTACGCGGCACTT
1 CGGTGCAACTCTACGCGGCACTT
* * *
2974551 CGGTGTAATTCTACGTGGCACTT
1 CGGTGCAACTCTACGCGGCACTT
2974574 CGGTGCA
1 CGGTGCA
2974581 TTTATACGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.26
Consensus pattern (23 bp):
CGGTGCAACTCTACGCGGCACTT
Found at i:2974588 original size:23 final size:23
Alignment explanation
Indices: 2974528--2974588 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
2974518 TATGGCACAA
* *
2974528 CGGTGCAACTCTACGCGGCACTT
1 CGGTGCAATTATACGCGGCACTT
* * *
2974551 CGGTGTAATTCTACGTGGCACTT
1 CGGTGCAATTATACGCGGCACTT
*
2974574 CGGTGCATTTATACG
1 CGGTGCAATTATACG
2974589 AGCTGTGGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
CGGTGCAATTATACGCGGCACTT
Found at i:2976093 original size:18 final size:17
Alignment explanation
Indices: 2976048--2976093 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2976038 TTGATGGTGT
2976048 AATTATATTTTAAATTAC
1 AATTAT-TTTTAAATTAC
* *
2976066 AAGTAGTTTTGAAATTAC
1 AATTA-TTTTTAAATTAC
2976084 AATTATTTTT
1 AATTATTTTT
2976094 TAAGAAACTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 4 0.17
18 18 0.78
19 1 0.04
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (17 bp):
AATTATTTTTAAATTAC
Found at i:2981835 original size:17 final size:17
Alignment explanation
Indices: 2981813--2981868 Score: 103
Period size: 17 Copynumber: 3.3 Consensus size: 17
2981803 AACGGTCAAC
2981813 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2981830 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2981847 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
2981864 AGTCA
1 GGTCA
2981869 GACCGGTCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.14, C:0.23, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:2981901 original size:20 final size:22
Alignment explanation
Indices: 2981877--2981936 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 22
2981867 CAGACCGGTC
*
2981877 AAAACCGGTTC-GAATCGGTTG
1 AAAACCGGTTCAGAACCGGTTG
2981898 -AAACCGG-TCAGAACCGGTTG
1 AAAACCGGTTCAGAACCGGTTG
2981918 AAAACCGGTT-A-AACCGGTT
1 AAAACCGGTTCAGAACCGGTT
2981937 TCCAGCAGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
19 2 0.06
20 24 0.69
21 8 0.23
22 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (22 bp):
AAAACCGGTTCAGAACCGGTTG
Found at i:2981925 original size:11 final size:10
Alignment explanation
Indices: 2981878--2981936 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
2981868 AGACCGGTCA
2981878 AAACCGGTTCG
1 AAACCGGTT-G
*
2981889 -AATCGGTTG
1 AAACCGGTTG
*
2981898 AAACCGG-TC
1 AAACCGGTTG
2981907 AGAACCGGTTG
1 A-AACCGGTTG
2981918 AAAACCGGTT-
1 -AAACCGGTTG
2981928 AAACCGGTT
1 AAACCGGTT
2981937 TCCAGCAGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
9 12 0.30
10 18 0.45
11 9 0.22
12 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (10 bp):
AAACCGGTTG
Found at i:2981932 original size:30 final size:30
Alignment explanation
Indices: 2981870--2981935 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
2981860 GTCGAGTCAG
*
2981870 ACCGGTCAAAACCGGTTCGAATCGGTTGAA
1 ACCGGTCAAAACCGGTTCGAACCGGTTGAA
*
2981900 ACCGGTCAGAACCGGTT-GAAAACCGGTT-AA
1 ACCGGTCAAAACCGGTTCG--AACCGGTTGAA
2981930 ACCGGT
1 ACCGGT
2981936 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 1 0.03
30 24 0.75
31 7 0.22
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.18
Consensus pattern (30 bp):
ACCGGTCAAAACCGGTTCGAACCGGTTGAA
Found at i:2988463 original size:17 final size:17
Alignment explanation
Indices: 2988441--2988496 Score: 112
Period size: 17 Copynumber: 3.3 Consensus size: 17
2988431 AGCGGTCAAC
2988441 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2988458 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2988475 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2988492 GGTCA
1 GGTCA
2988497 GACCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.12, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:2988468 original size:7 final size:7
Alignment explanation
Indices: 2988414--2988451 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
2988404 GTCAAAGAAA
2988414 GTCAACG
1 GTCAACG
2988421 GTCAACG
1 GTCAACG
*
2988428 GTCAGCG
1 GTCAACG
2988435 GTCAACG
1 GTCAACG
2988442 GTCAACG
1 GTCAACG
2988449 GTC
1 GTC
2988452 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.24, C:0.29, G:0.32, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:2988530 original size:10 final size:10
Alignment explanation
Indices: 2988517--2988573 Score: 73
Period size: 10 Copynumber: 5.7 Consensus size: 10
2988507 ATCGGTTCAG
2988517 ACCGGTTGAA
1 ACCGGTTGAA
2988527 ACCGGTTGAA
1 ACCGGTTGAA
*
2988537 ACCGG-TCAGA
1 ACCGGTTGA-A
2988547 ACCGGTTGAAA
1 ACCGGTTG-AA
2988558 ACCGGTT-AA
1 ACCGGTTGAA
2988567 ACCGGTT
1 ACCGGTT
2988574 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
9 11 0.26
10 21 0.50
11 9 0.21
12 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.19
Consensus pattern (10 bp):
ACCGGTTGAA
Found at i:2988553 original size:30 final size:29
Alignment explanation
Indices: 2988498--2988572 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 29
2988488 GTCGGGTCAG
* *
2988498 ACCGGTCAAATCGGTTCAGACCGGTTG-AA
1 ACCGGTTAAACCGG-TCAGACCGGTTGAAA
2988527 ACCGGTTGAAACCGGTCAGAACCGGTTGAAA
1 ACCGGTT-AAACCGGTCAG-ACCGGTTGAAA
2988558 ACCGGTTAAACCGGT
1 ACCGGTTAAACCGGT
2988573 TTCCAGCAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
29 10 0.24
30 22 0.54
31 9 0.22
ACGTcount: A:0.29, C:0.24, G:0.28, T:0.19
Consensus pattern (29 bp):
ACCGGTTAAACCGGTCAGACCGGTTGAAA
Found at i:2991069 original size:17 final size:17
Alignment explanation
Indices: 2991047--2991080 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2991037 TAGTTGGGCA
2991047 CTCCTCCTTTCCTTGCG
1 CTCCTCCTTTCCTTGCG
2991064 CTCCTCCTTTCCTTGCG
1 CTCCTCCTTTCCTTGCG
2991081 GGAGGGCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.47, G:0.12, T:0.41
Consensus pattern (17 bp):
CTCCTCCTTTCCTTGCG
Found at i:2999561 original size:16 final size:16
Alignment explanation
Indices: 2999523--2999554 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2999513 TTAAAGCATG
2999523 GAGAGTTTGGAGACAC
1 GAGAGTTTGGAGACAC
*
2999539 GAGAGTTTTGAGACAC
1 GAGAGTTTGGAGACAC
2999555 ATGAGTTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.12, G:0.34, T:0.22
Consensus pattern (16 bp):
GAGAGTTTGGAGACAC
Found at i:3003436 original size:17 final size:18
Alignment explanation
Indices: 3003411--3003454 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
3003401 TTGTTGAAGG
*
3003411 ATAACTTAAAC-AAATTA
1 ATAAATTAAACTAAATTA
*
3003428 ATAAATTAAACTTAATTA
1 ATAAATTAAACTAAATTA
*
3003446 ATAATTTAA
1 ATAAATTAA
3003455 GCCTATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAAATTAAACTAAATTA
Found at i:3003592 original size:20 final size:20
Alignment explanation
Indices: 3003559--3003614 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
3003549 AAACTACACA
3003559 ATTTCATATTTTTTCACTTTT
1 ATTTCAT-TTTTTTCACTTTT
3003580 ATTTCATTTTTTTCACTTTT
1 ATTTCATTTTTTTCACTTTT
3003600 ATTTCATTTTTTTCA
1 ATTTCATTTTTTTCA
3003615 TTCATTTCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 28 0.80
21 7 0.20
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTCATTTTTTTCACTTTT
Found at i:3003593 original size:9 final size:9
Alignment explanation
Indices: 3003560--3003616 Score: 69
Period size: 10 Copynumber: 5.8 Consensus size: 9
3003550 AACTACACAA
3003560 TTTCATATTT
1 TTTCAT-TTT
3003570 TTTCACTTTT
1 TTTCA-TTTT
3003580 ATTTCATTTT
1 -TTTCATTTT
3003590 TTTCACTTTT
1 TTTCA-TTTT
3003600 ATTTCATTTT
1 -TTTCATTTT
3003610 TTTCATT
1 TTTCATT
3003617 CATTTCCCGA
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
9 12 0.28
10 20 0.47
11 11 0.26
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTCATTTT
Found at i:3004219 original size:27 final size:26
Alignment explanation
Indices: 3004164--3004222 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
3004154 ATATTTTTGC
*
3004164 AAGTTCAATTAACTAAAAATGGTACTA
1 AAGTTCAATTAACTAAAAA-GATACTA
3004191 AAGTTCAATTAACTAAAAA-ATACAATA
1 AAGTTCAATTAACTAAAAAGATAC--TA
3004218 AAGTT
1 AAGTT
3004223 TTTCAAACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 3 0.10
27 26 0.90
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (26 bp):
AAGTTCAATTAACTAAAAAGATACTA
Found at i:3013201 original size:5 final size:5
Alignment explanation
Indices: 3013193--3013218 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3013183 AAGAGTAGAG
3013193 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
3013219 ACTAGAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:3021001 original size:2 final size:2
Alignment explanation
Indices: 3020996--3021089 Score: 161
Period size: 2 Copynumber: 47.0 Consensus size: 2
3020986 ACATTTTTTT
* * *
3020996 TA TA TA TA CA TT TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3021038 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3021080 TA TA TA TA TA
1 TA TA TA TA TA
3021090 GTTTACAAAT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3021144 original size:39 final size:36
Alignment explanation
Indices: 3021075--3021388 Score: 253
Period size: 37 Copynumber: 8.2 Consensus size: 36
3021065 ATATATATAT
** **
3021075 ATATATATATATATAGTTTACAAATGATTTTTGAAA
1 ATATATATATATATAGTTTTTAAAACATTTTTGAAA
3021111 ATACGTATATGATATATAGTTTTTAAAACATTTTTTGAAA
1 ATA--TATAT-ATATATAGTTTTTAAAACA-TTTTTGAAA
* *
3021151 CTATATATATTATATAGTTTTTTAAAACATTTTCGAAA
1 ATATATATA-TATATAG-TTTTTAAAACATTTTTGAAA
*
3021189 AT-TATATAATATATAATTTTTAAAACATTTTTAGAAA
1 ATATATAT-ATATATAGTTTTTAAAACATTTTT-GAAA
*
3021226 AT-TATATATTATATAATTTTTGAAAACATTTTT-AAA
1 ATATATATA-TATATAGTTTTT-AAAACATTTTTGAAA
* *
3021262 ATAAATATAATATATAGTTTTTTAAATCA-TTTTGAAA
1 ATATATAT-ATATATAG-TTTTTAAAACATTTTTGAAA
* *
3021299 ACT-TATATAATATATTA-TTTTGGAAAAAATATTTTTGAAA
1 A-TATATAT-ATATA-TAGTTTT---TAAAACATTTTTGAAA
* *
3021339 ACAATTATATATTATATAGTTTTTCAAAAGCATGTTTGAAA
1 A-TA-TATATA-TATATAGTTTTT-AAAA-CATTTTTGAAA
3021380 ATATATATA
1 ATATATATA
3021389 AATTTAAAAT
Statistics
Matches: 231, Mismatches: 21, Indels: 49
0.77 0.07 0.16
Matches are distributed among these distances:
36 32 0.14
37 64 0.28
38 47 0.20
39 36 0.16
40 26 0.11
41 13 0.06
42 13 0.06
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (36 bp):
ATATATATATATATAGTTTTTAAAACATTTTTGAAA
Found at i:3026516 original size:18 final size:19
Alignment explanation
Indices: 3026488--3026523 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3026478 TCAATAAAAG
3026488 TTGTCTGTCAACAAACAAC
1 TTGTCTGTCAACAAACAAC
*
3026507 TTGT-TGTCAATAAACAA
1 TTGTCTGTCAACAAACAA
3026524 TTTTCCACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (19 bp):
TTGTCTGTCAACAAACAAC
Found at i:3026694 original size:106 final size:106
Alignment explanation
Indices: 3026509--3027913 Score: 2467
Period size: 106 Copynumber: 13.3 Consensus size: 106
3026499 CAAACAACTT
* * * * *
3026509 GTTGTCAATAAACAA-TTTTCCACTTCTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
1 GTTGTCAACAAACAACTTCTCAATTTC-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
*
3026573 TCCAGACAACGCAAGTTCAACTTCACGAAGAAGGGACCGCTG
65 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
3026615 GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
1 GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
3026680 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
66 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
*
3026721 GTTGTCAACAAACAACTTCTCAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
1 GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
3026786 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
66 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
3026827 GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
1 GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
3026892 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
66 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
*
3026933 GTTGTCAACAAACAACTTCTCAATTTTAGAGCCAATTTCAACTTCATC-ACGAAGGATATTGGAC
1 GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCA-CAACGAAGGATATTGGAC
3026997 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
65 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
* *
3027039 GTTGTCAACAAACAACTTCTCAATTTCTGACCCAATTTCAACTTCACAACGAAGGATATTGGACT
1 GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
*
3027104 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTG
66 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
* * * * *
3027145 GTTGTCAATAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACT
1 GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
3027210 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
66 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
3027251 GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
1 GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
3027316 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
66 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
*
3027357 GTTGTCAACAAACAACTTCTCAATTTTAGAGCCAATTAT-AACTTCACAACGAAGGATATTGGAC
1 GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATT-TCAACTTCACAACGAAGGATATTGGAC
*
3027421 CCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
65 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
3027463 GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
1 GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
*
3027528 CAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
66 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
*
3027569 GTTGTCAACAAACAACTTCTCAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
1 GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
3027634 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
66 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
* * *
3027675 GTTGTCAACAAACAACTTATCAATTTCTGACCCAATTTCAACTTCACAACGAAGGATATTGGACT
1 GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
3027740 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
66 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
* * * * * *
3027781 GTTGTCAATAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCATAGCGAAGGATATTGGACT
1 GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
*
3027846 CAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
66 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
* *
3027887 GTTGTCAATAAACAACTT-TCAACTTCA
1 GTTGTCAACAAACAACTTCTCAATTTCA
3027914 CGACGGAGGA
Statistics
Matches: 1244, Mismatches: 50, Indels: 11
0.95 0.04 0.01
Matches are distributed among these distances:
105 9 0.01
106 1225 0.98
107 10 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
GTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
Found at i:3028139 original size:81 final size:80
Alignment explanation
Indices: 3028007--3028325 Score: 359
Period size: 81 Copynumber: 3.9 Consensus size: 80
3027997 TCTGCCAACA
* * * * * * *
3028007 AAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAACTTAAGTCGA
1 AAAGACCCTCGAGTTCGACTACACTCAGCTCGAGGGCACATCATTTGCAGCATAACTCAAGGCGA
3028072 GAAGGGTTATCTGCC
66 GAAGGGTTATCTGCC
* * * * *
3028087 AACGACCCCCGAGTTCGATTACACTCAGCTCTGAGGGCACATCATTTACAGCATAACTCAAGGCT
1 AAAGACCCTCGAGTTCGACTACACTCAGCTC-GAGGGCACATCATTTGCAGCATAACTCAAGGCG
3028152 AGAAGGGTTATCTGCCAC
65 AGAAGGGTTATCTG-C-C
* * * * * * * *
3028170 AAAGACCTTCGAGTTCCACTCCACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
1 AAAGACCCTCGAGTTCGACTACACTCAGCTCGAGGGCACATCATTTGCAGCATAACTCAAGGCGA
*
3028235 GAAGGGTTATATGCC
66 GAAGGGTTATCTGCC
* * * * * *
3028250 AAAGACCCTTGAGTTCGATTGCACTCAACTTCGAGGGCACATCATTTGCAGCATAGCTCAAGGCA
1 AAAGACCCTCGAGTTCGACTACACTCAGC-TCGAGGGCACATCATTTGCAGCATAACTCAAGGCG
3028315 AGAAGGGTTAT
65 AGAAGGGTTAT
3028326 ATGTCAATAA
Statistics
Matches: 198, Mismatches: 37, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
80 49 0.25
81 83 0.42
82 40 0.20
83 26 0.13
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (80 bp):
AAAGACCCTCGAGTTCGACTACACTCAGCTCGAGGGCACATCATTTGCAGCATAACTCAAGGCGA
GAAGGGTTATCTGCC
Found at i:3028288 original size:163 final size:165
Alignment explanation
Indices: 3027990--3028325 Score: 491
Period size: 163 Copynumber: 2.0 Consensus size: 165
3027980 CCAACTCGAG
* * * *
3027990 AGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGC
1 AGGGTTATCTGCCAACAAAAGACCTTCGAGTTCCACTACACTCAGCTCAACGGCACATCATTTGC
* * *
3028055 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACGACCCCCGAGTTCGATTACACTCAGCTCTG
66 AGCATAACTTAAGTCGAGAAGGGTTATATGCCAAAGACCCCCGAGTTCGATTACACTCAACTCTG
*
3028120 AGGGCACATCATTTACAGCATAACTCAAGGCTAGA
131 AGGGCACATCATTTACAGCATAACTCAAGGCAAGA
*
3028155 AGGGTTATCTGCC-AC-AAAGACCTTCGAGTTCCACTCCACTCAGCTCCAA-GGCACATCATTTG
1 AGGGTTATCTGCCAACAAAAGACCTTCGAGTTCCACTACACTCAGCT-CAACGGCACATCATTTG
* ** *
3028217 CAGCATAGCTTAAGTCGAGAAGGGTTATATGCCAAAGACCCTTGAGTTCGATTGCACTCAACT-T
65 CAGCATAACTTAAGTCGAGAAGGGTTATATGCCAAAGACCCCCGAGTTCGATTACACTCAACTCT
* *
3028281 CGAGGGCACATCATTTGCAGCATAGCTCAAGGCAAGA
130 -GAGGGCACATCATTTACAGCATAACTCAAGGCAAGA
3028318 AGGGTTAT
1 AGGGTTAT
3028326 ATGTCAATAA
Statistics
Matches: 154, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
162 1 0.01
163 136 0.88
164 5 0.03
165 12 0.08
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.24
Consensus pattern (165 bp):
AGGGTTATCTGCCAACAAAAGACCTTCGAGTTCCACTACACTCAGCTCAACGGCACATCATTTGC
AGCATAACTTAAGTCGAGAAGGGTTATATGCCAAAGACCCCCGAGTTCGATTACACTCAACTCTG
AGGGCACATCATTTACAGCATAACTCAAGGCAAGA
Found at i:3028878 original size:2 final size:2
Alignment explanation
Indices: 3028873--3028960 Score: 158
Period size: 2 Copynumber: 44.0 Consensus size: 2
3028863 ACATTTTTTT
* *
3028873 TA TA TA TA CA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3028915 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3028957 TA TA
1 TA TA
3028961 GTTTACAAAT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3029241 original size:37 final size:35
Alignment explanation
Indices: 3028946--3029243 Score: 229
Period size: 36 Copynumber: 8.2 Consensus size: 35
3028936 ATATATATAT
** **
3028946 ATATATATATATATAGTTTACAAATGATTTTTGAAA
1 ATATATAT-TATATAGTTTTTAAAACATTTTTGAAA
*
3028982 ATACGTATATGATATAGTTTTTAAAACATTTTTTGAAA
1 ATA--TATATTATATAGTTTTTAAAACA-TTTTTGAAA
* *
3029020 CTATATA-TATATAGTTTTTAAAACATTTTCGAAA
1 ATATATATTATATAGTTTTTAAAACATTTTTGAAA
*
3029054 ATTATATAATATATAGTTTTTAAAACATTTTTAGAAA
1 A-TATATATTATATAGTTTTTAAAACATTTTT-GAAA
3029091 AT-TATA-TATA-A-TTTTTGAAAACA-TTTT-AAA
1 ATATATATTATATAGTTTTT-AAAACATTTTTGAAA
*
3029121 ATATATA-TATATAGTTTTTTAAATCA-TTTTGAAA
1 ATATATATTATATAG-TTTTTAAAACATTTTTGAAA
* * *
3029155 ACTTATATAATATATTA-TTTTGGAAAAAATATTTTTGAAAACA
1 A--TATATATTATA-TAGTTTT---TAAAACATTTTTG--AA-A
*
3029198 ATTATATATTATATAGTTTTTCAAAAGCATGTTTGAAA
1 A-TATATATTATATAGTTTTT-AAAA-CATTTTTGAAA
3029236 ATATATAT
1 ATATATAT
3029244 AAATTTAAAA
Statistics
Matches: 218, Mismatches: 18, Indels: 51
0.76 0.06 0.18
Matches are distributed among these distances:
30 5 0.02
31 8 0.04
32 10 0.05
33 16 0.07
34 21 0.10
35 27 0.12
36 40 0.18
37 29 0.13
38 20 0.09
39 6 0.03
40 9 0.04
41 8 0.04
42 17 0.08
43 2 0.01
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (35 bp):
ATATATATTATATAGTTTTTAAAACATTTTTGAAA
Found at i:3029367 original size:27 final size:27
Alignment explanation
Indices: 3029337--3029388 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3029327 AAAAAATATA
* *
3029337 TTTTTATATAT-ATATTTTTTTATTTC
1 TTTTTTTATATGATATTTATTTATTTC
*
3029363 TTTTTTTATTTGATATTTATTTATTT
1 TTTTTTTATATGATATTTATTTATTT
3029389 ATTTCGTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (27 bp):
TTTTTTTATATGATATTTATTTATTTC
Found at i:3035858 original size:25 final size:25
Alignment explanation
Indices: 3035824--3035874 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
3035814 GTACAGTACA
3035824 TAGAAATTCACCCGTATTTATGAAG
1 TAGAAATTCACCCGTATTTATGAAG
3035849 TAGAAATTCACCCGTATTTATGAAG
1 TAGAAATTCACCCGTATTTATGAAG
3035874 T
1 T
3035875 GCTGGAACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (25 bp):
TAGAAATTCACCCGTATTTATGAAG
Found at i:3037991 original size:20 final size:20
Alignment explanation
Indices: 3037966--3038006 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3037956 GACGTTCTCC
3037966 CTAAATTTTGTTGATAGATA
1 CTAAATTTTGTTGATAGATA
3037986 CTAAATTTTGTTGATAGATA
1 CTAAATTTTGTTGATAGATA
3038006 C
1 C
3038007 AGCAGCAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (20 bp):
CTAAATTTTGTTGATAGATA
Found at i:3047295 original size:182 final size:181
Alignment explanation
Indices: 3047006--3048543 Score: 2239
Period size: 182 Copynumber: 8.5 Consensus size: 181
3046996 TACAAATGAA
* * * * *
3047006 AAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGA-TAAACCGGTGTCATTATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCA-AATGATAAA
**
3047070 ACCGGTAAACCGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
65 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
* *
3047135 TAATTTAAAAGAGAAGAAGTTATAGCGCATATAAAGTGTCGATACTTTATAC
130 TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
* * * * *
3047187 AAATGTATCGATCCATAGAAATATAACAGGTAATAATATAACAAAACCGGTGTCATTATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCA-AATGATAAA
** *
3047252 ACCGGTAAACCGCTACCGGATATATTGAAAGTATCGATAAATTAATATAAGTATCGACACTTTTG
65 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
3047317 TAATTTAAAAGAGAAGAAG-T-TA-----T----AGTGTCGATACTTTATAC
130 TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
** * * * * *
3047358 AAATGTATCGATCCATAAAAATATAACAGATAATAATATAACAAAACCGGTGTCATTATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCA-AATGATAAA
* ** *
3047423 ACCGCTAAACCGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACATTTG
65 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
* *
3047488 TAATTTAAAAGAGAATAAGTTATAGCGCCTAAAAAGTGTCGATACTCTATAC
130 TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
*
3047540 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGATAAAACAGGTCTCGAAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTC-AAATGATAAA
3047605 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
65 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
3047670 -ATATTT-AAA-AG-AGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
130 TA-ATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
* * *
3047719 AAATGTATCGATCCATATCAATATAACAGGTAATAATATGACAAAACATGTATCGAAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTC-AAATGATAAA
** *
3047784 ACCGGTAAAAATATATCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
65 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
3047849 TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
130 TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
*
3047901 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGGAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTC-AAATGATAAA
* * *
3047966 ACCGGTAAAAAGATACCGGATATATTGAAAGTGTCGATAAATTAATATAACTATAGACACTTTTG
65 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
3048031 TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
130 TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
*
3048083 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACATGTCTCGAAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTC-AAATGATAAA
* * *
3048148 ACCGGTAAAAAGTTATCGGATATATTGAAAGTGTCGATAAATTAATATAATTATCGACACTTTT-
65 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
* *
3048212 TATATTTAAAAGAGAAGAAGTTATAGCGCATAAAAAGTGTCGATATTTTATAC
130 TA-ATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
*
3048265 AAATGTATCGATCCATAGCAATATAACATGTAATAATATGACAAAACAGGTCTCGAAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTC-AAATGATAAA
* * * *
3048330 ACCGGTAAAAAACTACCGGATATATTAAAAGTGTCGATAAATTAATATAAGTATCGATACTTTCG
65 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
* **
3048395 TAATTTAAAAGAGAAGAAATTATAAAGCCTAAAAAGTGTCGATACTTTATGA-
130 TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAT-AC
* * * * * * *
3048447 AAATGTATCGATCCATAACAATATAATAAGTAAAAATATAACAAAACCGGTATCAAAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTC-AAATGATAAA
** * * *
3048512 ACCGGTAAAGCGCTACTGGTTATGTTGAAAGT
65 ACCGGTAAAAAGCTACCGGATATATTGAAAGT
3048544 ATTGGTACTT
Statistics
Matches: 1258, Mismatches: 78, Indels: 41
0.91 0.06 0.03
Matches are distributed among these distances:
171 161 0.13
172 1 0.00
173 2 0.00
175 1 0.00
178 1 0.00
179 163 0.13
180 8 0.01
181 47 0.04
182 870 0.69
183 4 0.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (181 bp):
AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCAAATGATAAAA
CCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTGT
AATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
Found at i:3049639 original size:199 final size:197
Alignment explanation
Indices: 3049274--3049797 Score: 551
Period size: 199 Copynumber: 2.6 Consensus size: 197
3049264 ATTAGATTTT
* ** *
3049274 GTGTCAATACATTTATAACA-AGTATCGATCCC-AAAATCAAAGAGACCGATAATTATAATGTAA
1 GTGTCGATACATTTA-AA-ATAGTATCGATCCCGAAAA-CATCGAAACCGATAATTATAATGTAA
* * * *
3049337 TAGGTAAATTTCCAATGTAACCGGTAAAAATATACCGGGTTCATGAGAGAATGGGTCAACATAAA
63 TAGGTAAATTTACAATGTAACCGGTTAAAATATACC-GGTTAATGAGAGAATAGGTCAACATAAA
* * * * * *
3049402 GTATCGACACTTTTTTAATTTGTGTCGATACGTTTTTCCAAAATGAATG-GCAAACGAGGTGTAC
127 GTATCGACACTCTTTAAATATGTGTCGATACGTTTTTCCAAAAT-AAAGCACAAACGAGGTGCAC
3049466 GCATAAA
191 GCATAAA
* * * *
3049473 GTGTCGATACATTCGTAAAA-AGTATTGATCCTCG-AAACATCGAAATCGATAATTATTATATAA
1 GTGTCGATACATT--TAAAATAGTATCGATCC-CGAAAACATCGAAACCGATAATTATAATGTAA
* * * *
3049536 CAGGTAAATTTACAATGTAACCGGTTAAAATATACCGGTTAATTAGCA-AATAGGTCTACATTAT
63 TAGGTAAATTTACAATGTAACCGGTTAAAATATACCGGTTAATGAG-AGAATAGGTCAACA-TAA
* ** *
3049600 A-TATCGATACTCTTTAAATATGTGTCGATATTTTTTTTCCAAAATAAAGCACAAACGAGTTGCA
126 AGTATCGACACTCTTTAAATATGTGTCGATA-CGTTTTTCCAAAATAAAGCACAAACGAGGTGCA
3049664 CGCATAAA
190 CGCATAAA
* *
3049672 GTGTCGATACATTTAAAATTGTATCGATCCCGAAAACATCGAAACCGAT-ATACATAATGTAATA
1 GTGTCGATACATTTAAAATAGTATCGATCCCGAAAACATCGAAACCGATAAT-TATAATGTAATA
* * * * * * * *
3049736 GGTCAATTTATAATGTAACCGGTTTAAATTTACCGATTTTATGAGAAAATAGGTCAATATAA
65 GGTAAATTTACAATGTAACCGGTTAAAATATACCG-GTTAATGAGAGAATAGGTCAACATAA
3049798 GCGCTACCTA
Statistics
Matches: 269, Mismatches: 43, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
197 9 0.03
198 112 0.42
199 140 0.52
200 6 0.02
201 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (197 bp):
GTGTCGATACATTTAAAATAGTATCGATCCCGAAAACATCGAAACCGATAATTATAATGTAATAG
GTAAATTTACAATGTAACCGGTTAAAATATACCGGTTAATGAGAGAATAGGTCAACATAAAGTAT
CGACACTCTTTAAATATGTGTCGATACGTTTTTCCAAAATAAAGCACAAACGAGGTGCACGCATA
AA
Found at i:3049926 original size:23 final size:23
Alignment explanation
Indices: 3049876--3049920 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
3049866 TGCCTATTTT
*
3049876 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
3049899 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
3049921 TGTTATTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:3049938 original size:87 final size:87
Alignment explanation
Indices: 3049792--3049954 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
3049782 AAATAGGTCA
*
3049792 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATTTGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
3049857 CCGGTTAAATGCCTATTTTATT
66 CCAGTTAAATGCCTATTTTATT
*
3049879 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
3049944 CTAGTTAAATG
66 CCAGTTAAATG
3049955 ATATAATATA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCAGTTAAATGCCTATTTTATT
Found at i:3050191 original size:22 final size:21
Alignment explanation
Indices: 3050150--3050198 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
3050140 GGAAAAAATC
3050150 AAAAAA-GGGGGATTCGATCA
1 AAAAAAGGGGGGATTCGATCA
3050170 AAAAAAGGGGGAGCATTC-ATCA
1 AAAAAAGGGGG-G-ATTCGATCA
*
3050192 ACAAAAG
1 AAAAAAG
3050199 AAACCAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 6 0.24
21 4 0.16
22 11 0.44
23 4 0.16
ACGTcount: A:0.49, C:0.12, G:0.27, T:0.12
Consensus pattern (21 bp):
AAAAAAGGGGGGATTCGATCA
Found at i:3052307 original size:25 final size:24
Alignment explanation
Indices: 3052278--3052355 Score: 70
Period size: 24 Copynumber: 3.1 Consensus size: 24
3052268 TTTGAGGTGT
*
3052278 TATAAAAGTATTTAATAATTAATTTAA
1 TATAAAAATATTT--TAATTAA-TTAA
*
3052305 TA-ATAAATATATTTAATTAATTAA
1 TATAAAAATAT-TTTAATTAATTAA
*
3052329 TATAAAAATATTTT-TTTAAGTTAA
1 TATAAAAATATTTTAATTAA-TTAA
3052353 TAT
1 TAT
3052356 GTATAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
23 4 0.09
24 16 0.36
25 14 0.32
26 6 0.14
27 4 0.09
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (24 bp):
TATAAAAATATTTTAATTAATTAA
Found at i:3052330 original size:17 final size:16
Alignment explanation
Indices: 3052290--3052332 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
3052280 TAAAAGTATT
*
3052290 TAATAATTA-ATTTAA
1 TAATAAATATATTTAA
3052305 TAATAAATATATTTAA
1 TAATAAATATATTTAA
*
3052321 TTAATTAATATA
1 -TAATAAATATA
3052333 AAAATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 8 0.33
16 6 0.25
17 10 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATAAATATATTTAA
Found at i:3052352 original size:24 final size:23
Alignment explanation
Indices: 3052293--3052355 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 23
3052283 AAGTATTTAA
*
3052293 TAATTAATTTAATAATAAATATATT
1 TAATTAA-TTAAT-ATAAAAATATT
3052318 TAATTAATTAATATAAAAATATT
1 TAATTAATTAATATAAAAATATT
**
3052341 TTTTTAAGTTAATAT
1 TAATTAA-TTAATAT
3052356 GTATAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.44
24 12 0.35
25 7 0.21
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TAATTAATTAATATAAAAATATT
Found at i:3057036 original size:24 final size:23
Alignment explanation
Indices: 3056982--3057036 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
3056972 TTCTACCAAT
*
3056982 TTATATATAATTTTTATAAAAAA
1 TTATATATAAATTTTATAAAAAA
* * *
3057005 TTACATATAAATTTTATTAAAAG
1 TTATATATAAATTTTATAAAAAA
3057028 TATATATAT
1 T-TATATAT
3057037 TAAAAATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TTATATATAAATTTTATAAAAAA
Found at i:3057586 original size:29 final size:28
Alignment explanation
Indices: 3057553--3057688 Score: 121
Period size: 31 Copynumber: 4.6 Consensus size: 28
3057543 TAATTTATCG
3057553 AATATATTTTATTCTTATCTTAACTAGA
1 AATATATTTTATTCTTATCTTAACTAGA
* *
3057581 AGATATATTTTAATCTTATCTTAAACTTATA
1 A-ATATATTTTATTCTTATCTT-AAC-TAGA
* *
3057612 AATTATATTTTATTCTTATTTTAATTTAAGA
1 AA-TATATTTTATTCTTATCTTAA-CT-AGA
* * *
3057643 AATATATTTTTATTTTTATCTTAATTATAA
1 AATATA-TTTTATTCTTATCTTAACTA-GA
*
3057673 AAAATATTTTA-TCTTA
1 AATATATTTTATTCTTA
3057689 ATTTTCAAAT
Statistics
Matches: 89, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
28 5 0.06
29 25 0.28
30 19 0.21
31 40 0.45
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.54
Consensus pattern (28 bp):
AATATATTTTATTCTTATCTTAACTAGA
Found at i:3057667 original size:31 final size:30
Alignment explanation
Indices: 3057510--3057688 Score: 142
Period size: 29 Copynumber: 6.0 Consensus size: 30
3057500 TTAAAATCAC
* *
3057510 ATCTTAATATTAA-AAAAATATATTATT-TT
1 ATCTTAAT-TTAAGAAATATATTTTATTCTT
* *
3057539 TTCTTAATTTATCG-AATATATTTTATTCTT
1 ATCTTAATTTA-AGAAATATATTTTATTCTT
* *
3057569 ATCTTAA-CT-AGAAGATATATTTTAATCTT
1 ATCTTAATTTAAGAA-ATATATTTTATTCTT
* *
3057598 ATCTTAAACTTATA-AATTATATTTTATTCTT
1 ATCTT-AATTTA-AGAAATATATTTTATTCTT
* *
3057629 ATTTTAATTTAAGAAATATATTTTTATTTTT
1 ATCTTAATTTAAGAAATATA-TTTTATTCTT
3057660 ATCTTAATTATAA-AAA-ATATTTTA-TCTT
1 ATCTTAATT-TAAGAAATATATTTTATTCTT
3057688 A
1 A
3057689 ATTTTCAAAT
Statistics
Matches: 121, Mismatches: 17, Indels: 25
0.74 0.10 0.15
Matches are distributed among these distances:
27 1 0.01
28 8 0.07
29 44 0.36
30 24 0.20
31 38 0.31
32 5 0.04
33 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (30 bp):
ATCTTAATTTAAGAAATATATTTTATTCTT
Found at i:3057693 original size:60 final size:59
Alignment explanation
Indices: 3057527--3057693 Score: 171
Period size: 60 Copynumber: 2.8 Consensus size: 59
3057517 TATTAAAAAA
* * ** *
3057527 ATATATTATTTTT-TCTTAATTTATCGAATATATTTTATTCTTATCTTAACTAGAAGAT
1 ATATTTTATTTTTATCTTAACTTATAAAATATATTTTATTCTTATTTTAACTAGAAGAT
* * * *
3057585 ATATTTTAATCTTATCTTAAACTTATAAATTATATTTTATTCTTATTTTAATTTAAGAA-AT
1 ATATTTTATTTTTATCTT-AACTTATAAAATATATTTTATTCTTATTTTAA-CT-AGAAGAT
*
3057646 ATATTTTTATTTTTATCTTAA-TTATAAAAAATATTTTA-TCTTAATTTT
1 ATA-TTTTATTTTTATCTTAACTTATAAAATATATTTTATTCTT-ATTTT
3057694 CAAATATTAT
Statistics
Matches: 90, Mismatches: 13, Indels: 10
0.80 0.12 0.09
Matches are distributed among these distances:
58 10 0.11
59 8 0.09
60 47 0.52
61 8 0.09
62 17 0.19
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (59 bp):
ATATTTTATTTTTATCTTAACTTATAAAATATATTTTATTCTTATTTTAACTAGAAGAT
Found at i:3058337 original size:31 final size:31
Alignment explanation
Indices: 3058302--3058366 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
3058292 TAATCACATC
* *
3058302 TTAA-TAAATAAAAAAAGGAAGTGATCATATA
1 TTAATTAAAT-AAAAAAGAAAATGATCATATA
*
3058333 TTAATTAAATAAAAACGAAAATGATCATATA
1 TTAATTAAATAAAAAAGAAAATGATCATATA
3058364 TTA
1 TTA
3058367 TATTTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.29
Consensus pattern (31 bp):
TTAATTAAATAAAAAAGAAAATGATCATATA
Found at i:3059973 original size:35 final size:36
Alignment explanation
Indices: 3059928--3060048 Score: 147
Period size: 35 Copynumber: 3.4 Consensus size: 36
3059918 GGCAACAAAC
* *
3059928 TTTTAAAAAATGATTTTCAAAATTTGGTAAATGTTT
1 TTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
3059964 TTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 TTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* * * *
3059999 CTTTGAAAAATAATTTTTTAAAGTTTGGTAGATG-TT
1 TTTTGAAAAATGA-TTTTCAAAGTTTGGTAAATGTTT
*
3060035 TGTTGAAAAATGAT
1 TTTTGAAAAATGAT
3060049 AATGGGATAA
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
35 33 0.46
36 21 0.29
37 18 0.25
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (36 bp):
TTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:3064659 original size:37 final size:36
Alignment explanation
Indices: 3064560--3064679 Score: 156
Period size: 35 Copynumber: 3.3 Consensus size: 36
3064550 TGGCAACCAA
3064560 CTTTGAAAAAATGGTTTTT-AAAGTTTGGTAAATGTTT
1 CTTTG-AAAAAT-GTTTTTCAAAGTTTGGTAAATGTTT
* *
3064597 CTTTG-AAAATGGTTTTCAATGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
*
3064632 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GTTTTTCAAAGTTTGGTAAATGTTT
*
3064669 -GTTGAAAAATG
1 CTTTGAAAAATG
3064680 ATAATGGGAT
Statistics
Matches: 74, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
34 5 0.07
35 28 0.38
36 14 0.19
37 27 0.36
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:3066026 original size:39 final size:39
Alignment explanation
Indices: 3065972--3066052 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
3065962 TATTGAATAT
* *
3065972 AATATAATTTTAAATTTTCAATACCTACAAGCATTTGTA
1 AATATAATTTTAAATTTTAAATACCTACAAGCATTTATA
* **
3066011 AATATAGTTTTAAATTTTAAATACCTACGTGCATTTATA
1 AATATAATTTTAAATTTTAAATACCTACAAGCATTTATA
3066050 AAT
1 AAT
3066053 TTAAAATTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (39 bp):
AATATAATTTTAAATTTTAAATACCTACAAGCATTTATA
Found at i:3066494 original size:31 final size:31
Alignment explanation
Indices: 3066459--3066521 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
3066449 TAGAATATAT
3066459 ATTATTTTGTAATCACATTAGCTTAATAAAA
1 ATTATTTTGTAATCACATTAGCTTAATAAAA
*
3066490 ATTATTTTGTAATCACCTTAGCTTAATAAAA
1 ATTATTTTGTAATCACATTAGCTTAATAAAA
3066521 A
1 A
3066522 AACATTAAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.41
Consensus pattern (31 bp):
ATTATTTTGTAATCACATTAGCTTAATAAAA
Found at i:3073674 original size:20 final size:20
Alignment explanation
Indices: 3073627--3073675 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
3073617 AAACTTAAAT
*
3073627 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
3073647 CCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
3073667 TCGCAACGC
1 TCGCAACGC
3073676 TATTTTAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.08
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:3073713 original size:20 final size:20
Alignment explanation
Indices: 3073684--3073767 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
3073674 GCTATTTTAG
*
3073684 TTTCGTGTTGCGATTTTAAT
1 TTTCGCGTTGCGATTTTAAT
*
3073704 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTAAT
* *
3073724 GTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTAAT
* *
3073744 TTTCGCGTTGCGAATTTAAG
1 TTTCGCGTTGCGATTTTAAT
3073764 TTTC
1 TTTC
3073768 AGAAACTACT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.13, C:0.17, G:0.21, T:0.49
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAT
Found at i:3075976 original size:21 final size:21
Alignment explanation
Indices: 3075897--3075994 Score: 76
Period size: 21 Copynumber: 4.7 Consensus size: 21
3075887 ATGCACCTAT
* * *
3075897 CATCATTCAAAAGGCGCC-TC
1 CATCGTTCAAGAGGCCCCTTC
*
3075917 CTATCGTTCAAGAGGCCTC-TC
1 C-ATCGTTCAAGAGGCCCCTTC
* * *
3075938 TCATCATTGAAGATGCCCCTTC
1 -CATCGTTCAAGAGGCCCCTTC
*
3075960 CACCGTTCAAGAGGCCCCTGT-
1 CATCGTTCAAGAGGCCCCT-TC
3075981 CATCGTTCAAGAGG
1 CATCGTTCAAGAGG
3075995 TCCCGCCCGC
Statistics
Matches: 61, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 1 0.02
21 56 0.92
22 4 0.07
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.24
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTTC
Found at i:3077892 original size:18 final size:18
Alignment explanation
Indices: 3077869--3077904 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3077859 AGGCCGGTTG
*
3077869 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
3077887 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
3077905 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:3080980 original size:16 final size:15
Alignment explanation
Indices: 3080958--3080996 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3080948 GAAATCATTG
3080958 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
3080974 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
3080989 AAAAATTA
1 AAAAATTA
3080997 GAGACGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:3081176 original size:19 final size:20
Alignment explanation
Indices: 3081152--3081284 Score: 92
Period size: 20 Copynumber: 6.7 Consensus size: 20
3081142 AACTAAAACC
3081152 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAAATTGAAATTCG
*
3081171 TGTTGCG-AATTCGAAAATCG
1 TGTTGCGAAATT-GAAATTCG
* *
3081191 AGTTGCGAATTTGAAATTC-
1 TGTTGCGAAATTGAAATTCG
* *
3081210 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAAATTGAAATTC-G
* * ** *
3081231 TGTTGTGAATTTGACTTTTG
1 TGTTGCGAAATTGAAATTCG
* ** *
3081251 TGTTGCGAATTTGACTTTTG
1 TGTTGCGAAATTGAAATTCG
*
3081271 TGTTGCGAATTTGA
1 TGTTGCGAAATTGA
3081285 CTTATGTGTT
Statistics
Matches: 99, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.04
19 26 0.26
20 52 0.53
21 17 0.17
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.41
Consensus pattern (20 bp):
TGTTGCGAAATTGAAATTCG
Found at i:3081197 original size:20 final size:19
Alignment explanation
Indices: 3081172--3081231 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
3081162 TTAAATTCGT
*
3081172 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAAATC-A
*
3081192 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAAATCA
*
3081211 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAAATCA
3081230 GT
1 GT
3081232 GTTGTGAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 22 0.58
20 16 0.42
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (19 bp):
GTTGCGAATTTGAAAATCA
Found at i:3081215 original size:39 final size:41
Alignment explanation
Indices: 3081153--3081244 Score: 109
Period size: 39 Copynumber: 2.3 Consensus size: 41
3081143 ACTAAAACCT
* *
3081153 GTTGCGAAATT-AAATTCGTGTTGCGAATTCGAAAATC-GA
1 GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCAGA
* * *
3081192 GTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCAGA
*
3081232 GTTGTGAATTTGA
1 GTTGCGAATTTGA
3081245 CTTTTGTGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 26 0.58
40 19 0.42
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (41 bp):
GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCAGA
Found at i:3081255 original size:20 final size:20
Alignment explanation
Indices: 3081211--3081298 Score: 122
Period size: 20 Copynumber: 4.3 Consensus size: 20
3081201 TTGAAATTCA
* **
3081211 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTG-ACTTTTGT
*
3081232 GTTGTGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
3081252 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
*
3081272 GTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTTTTGT
3081292 GTTGCGA
1 GTTGCGA
3081299 TTTACAAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
20 50 0.82
21 11 0.18
ACGTcount: A:0.19, C:0.09, G:0.26, T:0.45
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:3081274 original size:40 final size:41
Alignment explanation
Indices: 3081170--3081298 Score: 129
Period size: 40 Copynumber: 3.2 Consensus size: 41
3081160 AATTAAATTC
* * * **
3081170 GTGTTGCGAATTCGAAAATC-GAGTTGCGAATTTGAAAT-T
1 GTGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTTAT
** * *
3081209 CAGTTGCGAATTTGAAATTCAGTGTTGTGAATTTGACTTTT
1 GTGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTTAT
* **
3081250 GTGTTGCGAATTTG-ACTTTTGTGTTGCGAATTTGACTTAT
1 GTGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTTAT
3081290 GTGTTGCGA
1 GTGTTGCGA
3081299 TTTACAAATT
Statistics
Matches: 73, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
39 16 0.22
40 44 0.60
41 13 0.18
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.41
Consensus pattern (41 bp):
GTGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTTAT
Found at i:3081316 original size:40 final size:42
Alignment explanation
Indices: 3081170--3081318 Score: 127
Period size: 40 Copynumber: 3.7 Consensus size: 42
3081160 AATTAAATTC
* * **
3081170 GTGTTGCGAATTCGA-AAA-TCGAGTTGCGAATTTGAAAT-T
1 GTGTTGCGAATTTGACAAATTCGTGTTGCGAATTTGACTTAT
** * *
3081209 CAGTTGCGAATTTG--AAATTCAGTGTTGTGAATTTGACTTTT
1 GTGTTGCGAATTTGACAAATTC-GTGTTGCGAATTTGACTTAT
* *
3081250 GTGTTGCGAATTTGAC--TTTTGTGTTGCGAATTTGACTTAT
1 GTGTTGCGAATTTGACAAATTCGTGTTGCGAATTTGACTTAT
*
3081290 GTGTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 GTGTTGCGAATTTGACAAATTCGTGTTGCGA
3081319 TTGACATATT
Statistics
Matches: 87, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
38 5 0.06
39 17 0.20
40 50 0.57
41 15 0.17
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.40
Consensus pattern (42 bp):
GTGTTGCGAATTTGACAAATTCGTGTTGCGAATTTGACTTAT
Found at i:3081335 original size:20 final size:20
Alignment explanation
Indices: 3081292--3081338 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
3081282 TGACTTATGT
* **
3081292 GTTGCGATTTACAAATTCGC
1 GTTGCGATTGACAAATTCAA
*
3081312 GTTGCGATTGACATATTCAA
1 GTTGCGATTGACAAATTCAA
3081332 GTTGCGA
1 GTTGCGA
3081339 ATTTGGAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (20 bp):
GTTGCGATTGACAAATTCAA
Found at i:3081829 original size:13 final size:14
Alignment explanation
Indices: 3081806--3081837 Score: 55
Period size: 14 Copynumber: 2.2 Consensus size: 14
3081796 TTAAAATTTA
3081806 AAAATATAAAATATC
1 AAAATA-AAAATATC
3081821 AAAATAAAAATATC
1 AAAATAAAAATATC
3081835 AAA
1 AAA
3081838 TCAAACTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATAAAAATATC
Found at i:3081832 original size:14 final size:15
Alignment explanation
Indices: 3081785--3081837 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
3081775 TGTTTGGATT
* *
3081785 AATATTAAAATTTAA
1 AATATCAAAATATAA
* *
3081800 AATTTAAAAATATAA
1 AATATCAAAATATAA
3081815 AATATCAAAATA-AA
1 AATATCAAAATATAA
3081829 AATATCAAA
1 AATATCAAA
3081838 TCAAACTACA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
14 11 0.33
15 22 0.67
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (15 bp):
AATATCAAAATATAA
Found at i:3082224 original size:15 final size:15
Alignment explanation
Indices: 3082204--3082285 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
3082194 TTCCAGAAAA
3082204 TGAATTACTGGAATT
1 TGAATTACTGGAATT
3082219 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
3082234 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
3082249 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
3082264 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
3082278 TGAATTAC
1 TGAATTAC
3082286 ATTTCTGTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:3082238 original size:30 final size:30
Alignment explanation
Indices: 3082204--3082285 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
3082194 TTCCAGAAAA
**
3082204 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
3082234 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
3082264 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
3082286 ATTTCTGTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:3082263 original size:45 final size:44
Alignment explanation
Indices: 3082199--3082285 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
3082189 TGGTTTTCCA
**
3082199 GAAAATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACTG
3082244 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
3082286 ATTTCTGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (44 bp):
GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACTG
Found at i:3082291 original size:20 final size:20
Alignment explanation
Indices: 3082268--3082337 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
3082258 GGAATTTGAA
3082268 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
3082288 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
3082308 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
3082328 TTCTGGAAAA
1 TTCTGGAAAA
3082338 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:3082542 original size:27 final size:26
Alignment explanation
Indices: 3082504--3082566 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
3082494 TTTACTAAAA
* *
3082504 TATTATTGAAATATATAATAATATTAT
1 TATTATT-AAATATATAAAAAAATTAT
3082531 TCATTATTAAATATATAAAAAAATTAT
1 T-ATTATTAAATATATAAAAAAATTAT
3082558 TATATATTA
1 TAT-TATTA
3082567 TTAAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 2 0.06
27 24 0.75
28 6 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
TATTATTAAATATATAAAAAAATTAT
Found at i:3082657 original size:23 final size:23
Alignment explanation
Indices: 3082588--3082675 Score: 76
Period size: 22 Copynumber: 3.8 Consensus size: 23
3082578 ATATAATATC
*
3082588 TTATATTATTATATAATTGATT-ATT
1 TTATATTATTATA-AA-T-ATTAATA
*
3082613 TTATATATATTAAAAATA-TAATA
1 TTATAT-TATTATAAATATTAATA
3082636 TTATATTATTATAAATATTAATA
1 TTATATTATTATAAATATTAATA
* *
3082659 -AATA-TATTTTAAATATT
1 TTATATTATTATAAATATT
3082676 TTAATAATTA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
21 12 0.22
22 14 0.25
23 14 0.25
24 1 0.02
25 8 0.15
26 6 0.11
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
TTATATTATTATAAATATTAATA
Found at i:3082664 original size:45 final size:49
Alignment explanation
Indices: 3082573--3082671 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 49
3082563 ATTATTAAAA
* **
3082573 TAAAAATATAATATCTTATATTATTATATAATTGATTATTTTATATATAT
1 TAAAAATATAATA-CTTATATTATTATATAATTGATTAATAAATATATAT
*
3082623 TAAAAATATAATA-TTATATTATTATA-AA-T-ATTAATAAATATATTT
1 TAAAAATATAATACTTATATTATTATATAATTGATTAATAAATATATAT
3082668 TAAA
1 TAAA
3082672 TATTTTAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
45 16 0.36
46 1 0.02
47 2 0.04
48 13 0.29
50 13 0.29
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (49 bp):
TAAAAATATAATACTTATATTATTATATAATTGATTAATAAATATATAT
Found at i:3082671 original size:21 final size:22
Alignment explanation
Indices: 3082615--3082675 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
3082605 TGATTATTTT
* * *
3082615 ATATATATTAAAAATATAATATT
1 ATATATTTTAAATAT-TAATATA
*
3082638 ATATTATTATAAATATTAATA-A
1 ATA-TATTTTAAATATTAATATA
3082660 ATATATTTTAAATATT
1 ATATATTTTAAATATT
3082676 TTAATAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 12 0.38
22 3 0.09
23 8 0.25
24 9 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATATTTTAAATATTAATATA
Found at i:3082674 original size:43 final size:48
Alignment explanation
Indices: 3082573--3082666 Score: 117
Period size: 48 Copynumber: 2.0 Consensus size: 48
3082563 ATTATTAAAA
* *
3082573 TAAAAATATAATATCTTATATTATTATATAATTGATTATTTTATATATAT
1 TAAAAATATAATA-CTTATATTATTATATAATTGATTA-TATAAATATAT
3082623 TAAAAATATAATA-TTATATTATTATA-AA-T-ATTA-ATAAATATAT
1 TAAAAATATAATACTTATATTATTATATAATTGATTATATAAATATAT
3082666 T
1 T
3082667 TTAAATATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
43 9 0.21
45 4 0.10
46 1 0.02
47 2 0.05
48 13 0.31
50 13 0.31
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (48 bp):
TAAAAATATAATACTTATATTATTATATAATTGATTATATAAATATAT
Found at i:3082929 original size:42 final size:42
Alignment explanation
Indices: 3082864--3082978 Score: 176
Period size: 42 Copynumber: 2.7 Consensus size: 42
3082854 ATGAATTACA
* *
3082864 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
** * *
3082906 TTCTTAAAAACGAATTACGTGAAACAAATATGGGAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
3082948 TTCCGAAAAACGAATTACGTGAAACAAACAC
1 TTCCGAAAAACGAATTACGTGAAACAAACAC
3082979 TGTAATTCGA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (42 bp):
TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:3092275 original size:30 final size:30
Alignment explanation
Indices: 3092190--3092352 Score: 100
Period size: 30 Copynumber: 5.5 Consensus size: 30
3092180 GTAATAATTG
**
3092190 TTTTAGTCCTTTTAGTTGT-TGTTTTTACTA
1 TTTTAGTCC-TTTAAATGTCTGTTTTTACTA
** * * *
3092220 -TTTAACCCTTCAAGAT-TCTATTTTTTACTG
1 TTTTAGTCCTTTAA-ATGTCT-GTTTTTACTA
* *
3092250 TTTTAGTCCTTTAAATATCTGTTTTTGCTA
1 TTTTAGTCCTTTAAATGTCTGTTTTTACTA
* * * *
3092280 TTTTAATCCCTTAAATGTCTATTTTTAATA
1 TTTTAGTCCTTTAAATGTCTGTTTTTACTA
* * * * *
3092310 TTTTGGACCTTTAAATGTATGTTTTT-GTT
1 TTTTAGTCCTTTAAATGTCTGTTTTTACTA
*
3092339 TTTTGGTCCTTTAA
1 TTTTAGTCCTTTAA
3092353 GTTTCTGTAT
Statistics
Matches: 100, Mismatches: 28, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
28 4 0.04
29 22 0.22
30 61 0.61
31 13 0.13
ACGTcount: A:0.20, C:0.13, G:0.10, T:0.56
Consensus pattern (30 bp):
TTTTAGTCCTTTAAATGTCTGTTTTTACTA
Found at i:3092281 original size:60 final size:60
Alignment explanation
Indices: 3092209--3092336 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 60
3092199 TTTTAGTTGT
* * * * *
3092209 TGTTTTTACTA-TTTAA-CCCTTCAAGAT-TCTATTTTTTACTGTTTTAGTCCTTTAAATATC
1 TGTTTTTGCTATTTTAATCCCTT-AA-ATGTCTA-TTTTTAATATTTTAGACCTTTAAATATA
* *
3092269 TGTTTTTGCTATTTTAATCCCTTAAATGTCTATTTTTAATATTTTGGACCTTTAAATGTA
1 TGTTTTTGCTATTTTAATCCCTTAAATGTCTATTTTTAATATTTTAGACCTTTAAATATA
3092329 TGTTTTTG
1 TGTTTTTG
3092337 TTTTTTGGTC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
60 42 0.72
61 11 0.19
62 5 0.09
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (60 bp):
TGTTTTTGCTATTTTAATCCCTTAAATGTCTATTTTTAATATTTTAGACCTTTAAATATA
Found at i:3092365 original size:29 final size:30
Alignment explanation
Indices: 3092310--3092394 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 30
3092300 ATTTTTAATA
* * *
3092310 TTTTGGACCTTTAAATGTATGTTTTTGTT-
1 TTTTGGTCCTTTAAATTTATGTATTTGTTC
* *
3092339 TTTTGGTCCTTTAAGTTTCTGTATTTGTTC
1 TTTTGGTCCTTTAAATTTATGTATTTGTTC
* *
3092369 TTTTGCTCCTTTAACTTTATGTATTT
1 TTTTGGTCCTTTAAATTTATGTATTT
3092395 ACTGTTTAGC
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 24 0.51
30 23 0.49
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.60
Consensus pattern (30 bp):
TTTTGGTCCTTTAAATTTATGTATTTGTTC
Found at i:3092379 original size:30 final size:29
Alignment explanation
Indices: 3092317--3092394 Score: 93
Period size: 30 Copynumber: 2.7 Consensus size: 29
3092307 ATATTTTGGA
* * * *
3092317 CCTTTAAATGTATGTTTTTGTTTTTTGGT
1 CCTTTAACTTTATGTATTTGTTTTTTGCT
* *
3092346 CCTTTAAGTTTCTGTATTTGTTCTTTTGCT
1 CCTTTAACTTTATGTATTTGTT-TTTTGCT
3092376 CCTTTAACTTTATGTATTT
1 CCTTTAACTTTATGTATTT
3092395 ACTGTTTAGC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 18 0.44
30 23 0.56
ACGTcount: A:0.14, C:0.13, G:0.13, T:0.60
Consensus pattern (29 bp):
CCTTTAACTTTATGTATTTGTTTTTTGCT
Found at i:3094391 original size:30 final size:29
Alignment explanation
Indices: 3094353--3094412 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 29
3094343 GATTATATTG
*
3094353 TTTGTACTAACTTATTTTTCTC-TTGTGTT
1 TTTGTACTAACTCATTTTTCTCATT-TGTT
3094382 TTTGTTACTAACTCATTTTTCTCATTTGTT
1 TTTG-TACTAACTCATTTTTCTCATTTGTT
3094412 T
1 T
3094413 GTGTCATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 4 0.14
30 22 0.79
31 2 0.07
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (29 bp):
TTTGTACTAACTCATTTTTCTCATTTGTT
Found at i:3095616 original size:20 final size:20
Alignment explanation
Indices: 3095586--3095672 Score: 84
Period size: 20 Copynumber: 4.0 Consensus size: 20
3095576 ACGTTCCCTC
*
3095586 TCTTTGAGACCTTGAAACAT
1 TCTTTTAGACCTTGAAACAT
*
3095606 TCTTTTCGACCTTGAAACACT
1 TCTTTTAGACCTTGAAACA-T
3095627 GCCTCTCTTTGAGACCTTGAAACAT
1 ---TCT-TTT-AGACCTTGAAACAT
**
3095652 TCTTTGGGACCTTGAAACAT
1 TCTTTTAGACCTTGAAACAT
3095672 T
1 T
3095673 GTATTTATCT
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
20 31 0.55
21 3 0.05
22 3 0.05
24 3 0.05
25 4 0.07
26 12 0.21
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (20 bp):
TCTTTTAGACCTTGAAACAT
Found at i:3095649 original size:46 final size:46
Alignment explanation
Indices: 3095582--3095670 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
3095572 TTTGACGTTC
*
3095582 CCTCTCTTTGAGACCTTGAAACATTCTTTTCGACCTTGAAACACTG
1 CCTCTCTTTGAGACCTTGAAACATTCTTTGCGACCTTGAAACACTG
*
3095628 CCTCTCTTTGAGACCTTGAAACATTCTTTGGGACCTTGAAACA
1 CCTCTCTTTGAGACCTTGAAACATTCTTTGCGACCTTGAAACA
3095671 TTGTATTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.34
Consensus pattern (46 bp):
CCTCTCTTTGAGACCTTGAAACATTCTTTGCGACCTTGAAACACTG
Found at i:3096256 original size:25 final size:25
Alignment explanation
Indices: 3096236--3096306 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
3096226 GAAAAGAATT
** *
3096236 AAAGAAAAAAAGTAAAGAAAGAGCA
1 AAAGAAAAAAAACAAAGAAAGAACA
3096261 AAAGAAAAAAAACAAAGAAA-AA-A
1 AAAGAAAAAAAACAAAGAAAGAACA
*
3096284 GAGAGAAAATAAAAACAAAGAAA
1 -AAAG-AAA-AAAAACAAAGAAA
3096307 AAAAAACCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
23 1 0.03
24 4 0.10
25 21 0.54
26 13 0.33
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.03
Consensus pattern (25 bp):
AAAGAAAAAAAACAAAGAAAGAACA
Found at i:3096283 original size:11 final size:11
Alignment explanation
Indices: 3096267--3096381 Score: 55
Period size: 10 Copynumber: 10.5 Consensus size: 11
3096257 AGCAAAAGAA
3096267 AAAAAACAAAG
1 AAAAAACAAAG
*
3096278 -AAAAA-AGAG
1 AAAAAACAAAG
* *
3096287 AGAAAATAAA-
1 AAAAAACAAAG
* *
3096297 AACAAAGAAA-
1 AAAAAACAAAG
*
3096307 AAAAAACCAAG
1 AAAAAACAAAG
*
3096318 AGAAAAACAAATAA
1 A-AAAAAC-AA-AG
3096332 AAAGAAACAAAG
1 AAA-AAACAAAG
3096344 -AAAAA-AAAG
1 AAAAAACAAAG
*
3096353 CAAAAAA-AGGAG
1 -AAAAAACA-AAG
3096365 AAAAAACAAAG
1 AAAAAACAAAG
3096376 AAAAAA
1 AAAAAA
3096382 GAGGACAAGG
Statistics
Matches: 79, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
9 7 0.09
10 26 0.33
11 25 0.32
12 10 0.13
13 5 0.06
14 6 0.08
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (11 bp):
AAAAAACAAAG
Found at i:3096297 original size:15 final size:14
Alignment explanation
Indices: 3096261--3096381 Score: 83
Period size: 14 Copynumber: 8.7 Consensus size: 14
3096251 AGAAAGAGCA
3096261 AAAG-AAAAAAAAC
1 AAAGAAAAAAAAAC
*
3096274 AAAG---AAAAAAG
1 AAAGAAAAAAAAAC
*
3096285 AGAGAAAATAAAAAC
1 AAAGAAAA-AAAAAC
3096300 AAAGAAAAAAAAAC
1 AAAGAAAAAAAAAC
* *
3096314 CAAG--AGAAAAAC
1 AAAGAAAAAAAAAC
* *
3096326 AAATAAAAAGAAAC
1 AAAGAAAAAAAAAC
*
3096340 AAAGAAAAAAAAGC
1 AAAGAAAAAAAAAC
*
3096354 AAAAAAAGGAGAAAAAAC
1 -AAAGAA--A-AAAAAAC
3096372 AAAGAAAAAA
1 AAAGAAAAAA
3096382 GAGGACAAGG
Statistics
Matches: 82, Mismatches: 16, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
11 9 0.11
12 9 0.11
13 4 0.05
14 30 0.37
15 18 0.22
17 6 0.07
18 6 0.07
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (14 bp):
AAAGAAAAAAAAAC
Found at i:3096308 original size:16 final size:15
Alignment explanation
Indices: 3096216--3096360 Score: 69
Period size: 15 Copynumber: 9.1 Consensus size: 15
3096206 AGATCCAATC
*
3096216 AAAACAAAGAGAAAA
1 AAAACAAAGAAAAAA
* **
3096231 GAATTAAAGAAAAAA
1 AAAACAAAGAAAAAA
*
3096246 AGTAAAGAAAGAGCAAAAGA
1 A--AAACAAAGA--AAAA-A
* *
3096266 AAAA-AAACAAAGAA
1 AAAACAAAGAAAAAA
* * *
3096280 AAAAGAGAGAAAATA
1 AAAACAAAGAAAAAA
3096295 AAAACAAAGAAAAAA
1 AAAACAAAGAAAAAA
*
3096310 AAACCAAGAGAAAAACA
1 AAAACAA-AGAAAAA-A
3096327 AATAA-AAAGAAACAAA
1 AA-AACAAAGAAA-AAA
*
3096343 GAAAAAAAAGCAAAAAA
1 -AAAACAAAG-AAAAAA
3096360 A
1 A
3096361 GGAGAAAAAA
Statistics
Matches: 99, Mismatches: 18, Indels: 25
0.70 0.13 0.18
Matches are distributed among these distances:
14 5 0.05
15 38 0.38
16 16 0.16
17 27 0.27
18 7 0.07
19 4 0.04
20 2 0.02
ACGTcount: A:0.77, C:0.06, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAACAAAGAAAAAA
Found at i:3096323 original size:26 final size:25
Alignment explanation
Indices: 3096268--3096381 Score: 101
Period size: 26 Copynumber: 4.6 Consensus size: 25
3096258 GCAAAAGAAA
* * * *
3096268 AAAAACAAAGAAAAAAGAGAGAAAAT
1 AAAAACAAAGAAAAAA-AAACAAGAG
3096294 AAAAACAAAGAAAAAAAAACCAAGAG
1 AAAAACAAAGAAAAAAAAA-CAAGAG
* *
3096320 AAAAACAAATAAAAAGAAACAA-AG
1 AAAAACAAAGAAAAAAAAACAAGAG
* **
3096344 AAAAA-AAAG-CAAAAAAAGGAGA-
1 AAAAACAAAGAAAAAAAAACAAGAG
3096366 AAAAACAAAGAAAAAA
1 AAAAACAAAGAAAAAA
3096382 GAGGACAAGG
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
22 12 0.17
23 8 0.11
24 11 0.15
25 5 0.07
26 36 0.50
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (25 bp):
AAAAACAAAGAAAAAAAAACAAGAG
Found at i:3096376 original size:40 final size:38
Alignment explanation
Indices: 3096261--3096383 Score: 110
Period size: 39 Copynumber: 3.1 Consensus size: 38
3096251 AGAAAGAGCA
* *
3096261 AAAGAAAAAAAACAAAGAAAAAAGAGAGAAAATAA-AAAC
1 AAAGAAAAAAAAC-AAG-AAAAAGAGAAAAAAAAAGAAAC
* *
3096300 AAAGAAAAAAAAACCAAGAGAAAA-ACAAATAAAAAGAAAC
1 AAAG-AAAAAAAA-CAAGA-AAAAGAGAAAAAAAAAGAAAC
3096340 AAAGAAAAAAAAGCAA-AAAAAGGAGAAAAAACAAAGAAA-
1 AAAGAAAAAAAA-CAAGAAAAA-GAGAAAAAA-AAAGAAAC
3096379 AAAGA
1 AAAGA
3096384 GGACAAGGAG
Statistics
Matches: 70, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
37 4 0.06
38 1 0.01
39 34 0.49
40 30 0.43
41 1 0.01
ACGTcount: A:0.79, C:0.07, G:0.13, T:0.02
Consensus pattern (38 bp):
AAAGAAAAAAAACAAGAAAAAGAGAAAAAAAAAGAAAC
Found at i:3099448 original size:22 final size:22
Alignment explanation
Indices: 3099423--3099485 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
3099413 TGAGGGTTAT
3099423 ATAGGTCCTTCGGGACATATAC
1 ATAGGTCCTTCGGGACATATAC
3099445 ATAGGTCCTTCGGGAC--ATAC
1 ATAGGTCCTTCGGGACATATAC
3099465 ATGAGGTCCTTCGGGACATAT
1 AT-AGGTCCTTCGGGACATAT
3099486 TTCACATGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.16
21 14 0.37
22 16 0.42
23 2 0.05
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.27
Consensus pattern (22 bp):
ATAGGTCCTTCGGGACATATAC
Found at i:3099473 original size:21 final size:20
Alignment explanation
Indices: 3099423--3099484 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 20
3099413 TGAGGGTTAT
3099423 ATAGGTCCTTCGGGACATATAC
1 ATAGGTCCTTCGGGAC--ATAC
3099445 ATAGGTCCTTCGGGACATAC
1 ATAGGTCCTTCGGGACATAC
3099465 ATGAGGTCCTTCGGGACATA
1 AT-AGGTCCTTCGGGACATA
3099485 TTTCACATGC
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
20 6 0.15
21 17 0.44
22 16 0.41
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (20 bp):
ATAGGTCCTTCGGGACATAC
Found at i:3100652 original size:134 final size:134
Alignment explanation
Indices: 3100195--3101058 Score: 862
Period size: 134 Copynumber: 6.5 Consensus size: 134
3100185 CTTGCCATCC
* * * * * * * *
3100195 TCATCACATAGGAACCGTGTCATCCCC-GACCAGGCCTCATCATCATCTAGGAGCTGTGTCA-CT
1 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGACCTCCTCATCATGTAGGAGCCGTGTCACCC
* * * * * * * *
3100258 CTTGATAACCAAAT-GTACTCATCACGTAGGAACCGTATTAT---CATCCCTAAAGATGGTCTG-
66 CTAGATAACC-AGTCGTCCTCATCGCGTAGGAACCGTGTTATCACCATTCCTAAAGATGGCCAGA
* *
3100318 TCATCC
130 AC-TCT
* * * * * * *
3100324 TCATCGCGTAGGAACCGTGTCATCCCCCGACCAGATCTCCTCATCATGTAGGAGTCGTGTCACTC
1 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGACCTCCTCATCATGTAGGAGCCGTGTCACCC
* * * * * * * *
3100389 CT-GATAACCAGCCGTCCTCATCACGTAGAAATCATGTTAT---CATCCCTAAAGATGGTC--TA
66 CTAGATAACCAGTCGTCCTCATCGCGTAGGAACCGTGTTATCACCATTCCTAAAGATGGCCAGAA
*
3100448 -TCA
131 CTCT
* * * *
3100451 TCCTCATCGTATAGGAACCGTGTCATCCCC-GACCAGACCTCCTCATCATGTAGGAACTGTGTCA
1 TCATCA-CGTAT--GAGCCGTGTCATCCCCTGACCAGACCTCCTCATCATGTAGGAGCCGTGTCA
* *
3100515 CCCCTAGATAACCAGACGTCCTCATCGCGTAAGAACCGTGTTATCACCATTCCTAAAGATGGCCA
63 CCCCTAGATAACCAGTCGTCCTCATCGCGTAGGAACCGTGTTATCACCATTCCTAAAGATGGCCA
3100580 GAACTCT
128 GAACTCT
* * * * * * *
3100587 TCATTACATATGAGCCGTGCCATCCCCTGACCATACATCTTCATCACGTAGGAGCCGTGTCACCC
1 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGACCTCCTCATCATGTAGGAGCCGTGTCACCC
* * * *
3100652 CTAGATAACCAGTTGTCCTCATCGCTTAGGAACCGTGTTATCACCCTTCCTAATGAT-GCACAGA
66 CTAGATAACCAGTCGTCCTCATCGCGTAGGAACCGTGTTATCACCATTCCTAAAGATGGC-CAGA
3100716 ACTCT
130 ACTCT
*
3100721 TCATCACGTATGAGTCGTGTCATCCCCTGACCAGACCTCCTCATCATGTAGGAGCCGTGTCACCC
1 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGACCTCCTCATCATGTAGGAGCCGTGTCACCC
* * * * *
3100786 CCATATAACCAGTCGTCTTCATAGCGTAGGAACTGTGTTATCACCATTCCTAAAGATGGCCAGAA
66 CTAGATAACCAGTCGTCCTCATCGCGTAGGAACCGTGTTATCACCATTCCTAAAGATGGCCAGAA
3100851 CTCT
131 CTCT
* * *
3100855 TCATCACGTATGAGCCATGTCATCCCCCGACCAAACCTCCTCATCATGTAGGAGCCGTGTCACCC
1 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGACCTCCTCATCATGTAGGAGCCGTGTCACCC
* * * * * * *
3100920 TTAGATAACTAGTCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTCCCTGAAGATGTCCACGA
66 CTAGATAACCAGTCGTCCTCATCGCGTAGGAACCGTGTTATCACCATTCCTAAAGATGGCCA-GA
3100985 ACTCT
130 ACTCT
** * * * * **
3100990 TCATCACGTATGAGCAATGT-TTACCCTGACCAGATCTCCTCATCACGTAGGAGATGTGTCACCC
1 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGACCTCCTCATCATGTAGGAGCCGTGTCACCC
*
3101054 TTAGA
66 CTAGA
3101059 CGATTAGACC
Statistics
Matches: 621, Mismatches: 96, Indels: 31
0.83 0.13 0.04
Matches are distributed among these distances:
127 6 0.01
128 4 0.01
129 60 0.10
130 122 0.20
131 2 0.00
133 31 0.05
134 357 0.57
135 33 0.05
136 6 0.01
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (134 bp):
TCATCACGTATGAGCCGTGTCATCCCCTGACCAGACCTCCTCATCATGTAGGAGCCGTGTCACCC
CTAGATAACCAGTCGTCCTCATCGCGTAGGAACCGTGTTATCACCATTCCTAAAGATGGCCAGAA
CTCT
Found at i:3100780 original size:40 final size:40
Alignment explanation
Indices: 3100712--3100787 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
3100702 TAATGATGCA
* * * *
3100712 CAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCTGAC
1 CAGAACTCCTCATCACGTAGGAGCCGTGTCACCCCCTGAC
* *
3100752 CAGACCTCCTCATCATGTAGGAGCCGTGTCACCCCC
1 CAGAACTCCTCATCACGTAGGAGCCGTGTCACCCCC
3100788 ATATAACCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (40 bp):
CAGAACTCCTCATCACGTAGGAGCCGTGTCACCCCCTGAC
Found at i:3101260 original size:14 final size:14
Alignment explanation
Indices: 3101243--3101280 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3101233 TTTTATTTTT
3101243 TTATT-TTAAATTTA
1 TTATTATTAAA-TTA
*
3101257 TTATTATTATATTA
1 TTATTATTAAATTA
3101271 TTATTATTAA
1 TTATTATTAA
3101281 TAGTATGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATTATTAAATTA
Found at i:3101556 original size:3 final size:3
Alignment explanation
Indices: 3101550--3101601 Score: 70
Period size: 3 Copynumber: 17.0 Consensus size: 3
3101540 ATTTTAAAAT
3101550 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TATA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TTA
*
3101596 ATA TTA
1 TTA TTA
3101602 CAAAACCCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 36 0.82
4 6 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:3102944 original size:24 final size:22
Alignment explanation
Indices: 3102916--3102965 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
3102906 ATATATATAT
3102916 AATAAATAATAATTTATATTTTTC
1 AATAAAT--TAATTTATATTTTTC
* *
3102940 AATAAATTATTTTTTATTTTTC
1 AATAAATTAATTTATATTTTTC
3102962 AATA
1 AATA
3102966 TCGAAGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 17 0.71
24 7 0.29
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
AATAAATTAATTTATATTTTTC
Done.